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Implement a subset of the Common Workflow Language. #47

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Implement a subset of the Common Workflow Language. #47

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7099b14
Allow unit testing tool init to specify paths.
jmchilton Aug 18, 2017
84254d7
[WIP] Implement records - heterogenous dataset collections.
jmchilton May 18, 2020
da73bc8
Deal with workflow definitions without position fields.
jmchilton Nov 18, 2019
efa2e85
Add CWL conformance test data to Galaxy for testing.
jmchilton Jul 30, 2017
1df9a9c
Implement subset of the Common Workflow Language tool and workflow fo…
jmchilton Nov 5, 2020
c09de83
Generate Python test cases from CWL conformance tests
nsoranzo Jan 2, 2021
36c6fcc
CWL Testing and Runner Improvements.
jmchilton Nov 6, 2018
b8b6b39
Swap default for beta formats (do not include in Galaxy).
jmchilton Nov 20, 2019
26d1678
More logging messages... REMOVE LATER
jmchilton Mar 16, 2018
eaac097
WIP: Work toward Galaxy-flavored CWL tools.
jmchilton Apr 20, 2018
a608c11
[WIP] Implement client UI for field parameter type for CWL.
jmchilton Nov 17, 2019
38cbae7
Revert complex objectstore - for docker tests (needed for CWL).
jmchilton Jun 26, 2019
b738498
WORKAROUND TO GET TAR TO DIRECTORY WORKING AGAIN.
jmchilton Nov 7, 2020
95acd19
Create codeql-analysis.yml
mr-c Nov 8, 2021
f7ce1ed
Update .github/workflows/codeql-analysis.yml
mr-c Nov 8, 2021
8cd7307
Move CWL unit tests to test/unit/app/tools
nsoranzo Nov 8, 2021
bd5567e
Generate CWL conformance tests only when needed
nsoranzo Nov 9, 2021
937f2ee
Code cleanups
nsoranzo Nov 9, 2021
7e8ce0d
Fix CwlToolObjectTestCase unit test
nsoranzo Nov 9, 2021
82e111e
Ignore fals-y scatter_type
mvdbeek Nov 8, 2021
0600e71
Add fields parameter to create collection schema
mvdbeek Nov 9, 2021
7d89772
Fix non_data_connection workflows
mvdbeek Nov 9, 2021
9a06bd3
Use staged_addition/add_pending_items
mvdbeek Nov 9, 2021
665b018
Use allow_tool_state_corrections when running CWL conformance tests
mvdbeek Nov 9, 2021
1f019a6
Can't used TypedDict in python < 3.8
mvdbeek Nov 9, 2021
856be8a
Fix inverted worklfow ids and invocation ids
mvdbeek Nov 9, 2021
2d549f7
Fix nested collections getting reduced completely
mvdbeek Nov 10, 2021
d74ded5
Fix handling of uploaded_file_name
mvdbeek Nov 10, 2021
59c2c7a
Reenable check_upload_content
mvdbeek Nov 10, 2021
d59d343
Remove unneeded `check_upload_content=True`
nsoranzo Nov 10, 2021
7572b60
Undo persisting ephemeral collections
mvdbeek Nov 10, 2021
acf9575
Fix directory location tests
mvdbeek Nov 10, 2021
cba84c7
Consider a history not new once there are any items in it
mvdbeek Nov 10, 2021
0ccc310
Move num_hdas to else branch
mvdbeek Nov 11, 2021
62b96dd
Fix test_command_factory unit test
mvdbeek Nov 11, 2021
b58ffae
Make structure argument optional in subworkflow_progress
mvdbeek Nov 11, 2021
9063176
Fix typing issue
nsoranzo Nov 11, 2021
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2 changes: 1 addition & 1 deletion lib/galaxy_test/base/populators.py
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Original file line number Diff line number Diff line change
Expand Up @@ -314,7 +314,7 @@ def __init__(self, dataset_populator, workflow_populator, history_id, workflow_i
self.invocation_id = invocation_id

def _output_name_to_object(self, output_name):
invocation_response = self.dataset_populator._get(f"workflows/{self.invocation_id}/invocations/{self.workflow_id}")
invocation_response = self.dataset_populator._get(f"workflows/{self.workflow_id}/invocations/{self.invocation_id}")
api_asserts.assert_status_code_is(invocation_response, 200)
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We can just use the invocation ID now also.

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Good point, addressed in a commit that I'll push soon.

invocation = invocation_response.json()
return invocation_to_output(invocation, self.history_id, output_name)
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